Sodium in PDB 7b3n: Amip Amidase-3 From Thermus Parvatiensis

The structure of Amip Amidase-3 From Thermus Parvatiensis, PDB code: 7b3n was solved by S.Freitag-Pohl, E.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.68 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.539, 97.988, 148.723, 90, 90, 90
R / Rfree (%)	18.5 / 22.5

The structure of Amip Amidase-3 From Thermus Parvatiensis also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	5 atoms

The binding sites of Sodium atom in the Amip Amidase-3 From Thermus Parvatiensis (pdb code 7b3n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Amip Amidase-3 From Thermus Parvatiensis, PDB code: 7b3n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:35.5 occ:1.00 H A:SER67 2.1 29.6 1.0 H B:GLY103 2.1 27.7 1.0 O B:HOH352 2.7 29.1 1.0 OE1 B:GLU106 2.8 29.1 1.0 HA B:PRO102 2.8 29.7 1.0 N A:SER67 3.0 29.0 1.0 N B:GLY103 3.0 26.2 1.0 HB3 A:PRO65 3.0 29.4 1.0 HB2 A:LEU66 3.1 27.6 1.0 H A:LEU66 3.1 29.0 1.0 HB3 A:SER67 3.2 32.7 1.0 N A:LEU66 3.3 29.2 1.0 OG A:SER67 3.4 37.0 1.0 OE2 B:GLU106 3.5 30.6 1.0 CD B:GLU106 3.5 29.5 1.0 HG A:SER67 3.6 37.1 0.0 CA B:PRO102 3.6 28.6 1.0 CB A:SER67 3.6 32.4 1.0 HB2 A:PRO65 3.7 29.4 1.0 H B:GLU105 3.7 26.5 1.0 CB A:PRO65 3.7 28.7 1.0 HB3 B:GLU105 3.7 28.7 1.0 C A:PRO65 3.8 28.3 1.0 CA A:LEU66 3.8 29.1 1.0 C B:PRO102 3.8 30.6 1.0 C A:LEU66 3.8 31.2 1.0 HA2 B:GLY103 3.8 27.1 1.0 CB A:LEU66 3.8 26.8 1.0 CA A:SER67 3.9 29.3 1.0 H B:SER104 3.9 26.3 1.0 CA B:GLY103 3.9 28.2 1.0 HA A:PRO65 4.0 28.8 1.0 CA A:PRO65 4.0 29.0 1.0 O B:HOH359 4.0 40.5 1.0 O B:HIS101 4.1 29.1 1.0 H B:GLU106 4.1 26.1 1.0 H A:GLU68 4.2 28.6 1.0 N B:SER104 4.3 25.4 1.0 C B:GLY103 4.4 25.6 1.0 HG A:LEU66 4.4 28.2 1.0 HB3 B:PRO102 4.5 31.6 1.0 HB2 B:GLU105 4.5 28.7 1.0 N B:GLU105 4.5 25.3 1.0 HB3 A:LEU66 4.5 27.6 1.0 CB B:GLU105 4.5 29.0 1.0 HA A:SER67 4.5 29.8 1.0 N B:PRO102 4.5 29.2 1.0 O A:PRO65 4.6 30.2 1.0 HH2 B:TRP175 4.6 37.8 1.0 HB2 A:SER67 4.6 32.6 1.0 CB B:PRO102 4.7 32.1 1.0 CG A:LEU66 4.7 28.0 1.0 C B:HIS101 4.7 29.9 1.0 HA A:LEU66 4.7 29.1 1.0 HD11 A:LEU66 4.8 27.9 1.0 HA3 B:GLY103 4.8 27.1 1.0 N A:GLU68 4.9 27.0 1.0 HZ2 B:TRP175 4.9 38.0 1.0 N B:GLU106 4.9 24.8 1.0 C A:SER67 4.9 29.2 1.0 CG B:GLU106 5.0 31.9 1.0 O B:PRO102 5.0 30.9 1.0

Sodium binding site 2 out of 2 in the Amip Amidase-3 From Thermus Parvatiensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Amip Amidase-3 From Thermus Parvatiensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:50.6 occ:1.00 OD2 B:ASP136 2.4 45.4 1.0 OH C:TYR98 2.5 33.1 1.0 HA B:TYR133 2.6 30.2 1.0 OE1 C:GLU105 2.7 36.9 1.0 HE2 C:TYR98 2.7 31.9 1.0 O B:HOH336 2.7 40.7 1.0 HH C:TYR98 3.0 33.0 0.0 O B:HOH321 3.2 55.7 1.0 CG B:ASP136 3.2 40.1 1.0 CZ C:TYR98 3.3 32.1 1.0 CE2 C:TYR98 3.3 32.8 1.0 CD C:GLU105 3.3 34.0 1.0 OD1 B:ASP136 3.5 41.8 1.0 O C:HOH305 3.6 37.5 1.0 CA B:TYR133 3.6 30.4 1.0 OE2 C:GLU105 3.6 41.0 1.0 O B:HOH329 3.8 42.3 1.0 HB3 C:PRO123 3.8 31.0 1.0 O C:HOH339 3.9 43.4 1.0 HB2 B:TYR133 4.0 31.5 1.0 HB3 B:TYR133 4.1 31.5 1.0 O B:TYR133 4.1 31.6 1.0 CB B:TYR133 4.2 31.5 1.0 HB2 B:ASP136 4.2 34.8 1.0 O B:LEU132 4.2 27.7 1.0 N B:TYR133 4.3 28.9 1.0 HD3 C:PRO123 4.3 31.1 1.0 C B:TYR133 4.3 29.4 1.0 CB B:ASP136 4.4 34.0 1.0 HG3 C:PRO123 4.4 31.2 1.0 HB2 C:GLU105 4.4 29.9 1.0 CG C:GLU105 4.5 33.3 1.0 H B:ASP136 4.5 31.8 1.0 C B:LEU132 4.5 31.8 1.0 HG2 B:ARG131 4.5 37.1 1.0 HG3 C:GLU105 4.6 32.4 1.0 CE1 C:TYR98 4.6 29.7 1.0 CD2 C:TYR98 4.6 30.2 1.0 HG3 B:ARG131 4.7 37.0 1.0 CB C:PRO123 4.7 30.7 1.0 HB2 B:ASP135 4.8 33.2 1.0 HE B:ARG131 4.9 38.6 1.0 CG C:PRO123 4.9 31.7 1.0 H B:TYR133 4.9 30.0 1.0 CB C:GLU105 5.0 29.1 1.0 HE1 C:TYR98 5.0 30.1 1.0 HD2 C:TYR98 5.0 30.9 1.0 HB3 B:ASP136 5.0 34.8 1.0

S.Freitag-Pohl, E.Pohl. Amip Amidase-3 From Thermus Parvatiensis To Be Published.